Given two sequences, where one is a substring of the other, we define a substring 
alignment by matching the substring with the longer sequence and placing gaps everywhere
else. For example if the input is ACCTGTAGG and TGT then the substring alignment is

ACCTGTAGG
---TGT---

Write a Perl program that prints the substring alignment of two unaligned sequences in a FASTA file.
If no substring alignment exists then the program should print "No alignment found".

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You are given an alignment in ClustalW format. Write a Perl program to convert this to 
FASTA format and print it to the screen. The ClustalW format begins with the line 
"CLUSTAL W (1.83) multiple sequence alignment"  followed by two blank lines. 
Following that the alignment begins with the sequence name followed by spaces and the 
sequence on separate lines. However, the alignment is broken by sequence length into 
chunks of 60 characters. Below is an example of a ClustalW alignment. 
 
 
CLUSTAL W (1.83) multiple sequence alignment 
 
 
Seq1        AAAACAGGGTGATACAGATGCGATGCCCACACACCCCACACGGATTATTATTATATATAT 
Seq2        AAAACAGGGTGATACAGATGCTAATGCAACACACCAAACACGGATTATTAAAATCTATAT 
Seq3        AAAACAGGGTGATACAGATGCGATGCCCACACACCAAACACGGATTATTACCATGTATAT  
 
Seq1        GGCACGCAAAAATTATAGCGAGATGCTAGCATCAGACACAAAAAAAACGCGCGCTAGTCA 
Seq2        GGCACGCAACCCTTATAGCGAGATGCTAGCATCAGACACAAAAACGCCCGCGCGCTAGTC 
Seq3        GGCACGCAAGGGTTATAGCGAGATGCTAGCATCAGACACAAAACGGCCGCGCGCTAGTCA 
 
Seq1        AAGCGCGTAGCCC 
Seq2        AAGCGAATAGGGG 
Seq3        AACCCCGTAGCCC 
 
The resulting FASTA alignment would be 
 
>Seq1 
AAAACAGGGTGATACAGATGCGATGCCCACACACCCCACACGGATTATTATTATATATATGGCACGCAAAAATTATAGCGAGATGCTAGCATCAGACACAAAAAAAACGCGCGCTAGTCAAAGCGCGTAGCCC 
>Seq2 
AAAACAGGGTGATACAGATGCTAATGCAACACACCAAACACGGATTATTAAAATCTATATGGCACGCAACCCTTATAGCGAGATGCTAGCATCAGACACAAAAACGCCCGCGCGCTAGTCAAGCGAATAGGGG 
>Seq3 
AAAACAGGGTGATACAGATGCGATGCCCACACACCAAACACGGATTATTACCATGTATATGGCACGCAAGGGTTATAGCGAGATGCTAGCATCAGACACAAAACGGCCGCGCGCTAGTCAAACCCCGTAGCCC 

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Write a Perl program to compute the sum of pairs score of a multiple alignment with gaps. Your 
program will take as input a filename containing a FASTA alignment, the filename containing the
scoring matrix, the gap open, gap extension, and endgap penalties. When comparing two sequences
don't forget to ignore sites where both are gaps.

As an example, suppose the gap open, extension, and endgap penalties are -1, 0.1, and 0
respectively. Also suppose the match score is 1 and mismatch is 0. Then for the following
three sequence alignment the total score is

AACGTTGCAC
--CGTT--A-     
AACG----A-    

3.9 (for sequence 1 and 2) + 3.7 (for sequence 1 and 3) + 1.9 (for sequence 2 and 3) = 9.5

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Write a Perl subroutine that computes a maximal local aligned segment.
The input to the subroutine is

1. $q (query sequence)
2. $t (target sequence)
3. $kmer (a substring of length 3 that is contained in $q and $t)
4. $threshold (defined such that the maximal segment score will reduce by 
	       at most threshold if further extended)

For example, suppose the input $q and $t are

$t: ACCTGTAGG
$q: ATGTC

$kmer="TGT", and $threshold=-2. Also suppose the match score=10 and mismatch=-2. 

Then the kmer-hit has score 30. But if extended it becomes

CTGTA
ATGTC

which has a reduction of -4. This is less than the threshold -2 and so the maximal aligned
segment is 

TGT
TGT

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